WASHINGTON (Reuters) - U.S. Environmental Protection Agency officials are concerned that companies may be required to publicly disclose confidential data used in crafting government regulations, under an initiative by the agency's chief to eliminate "secret science," internal emails showed.

EPA Administrator Scott Pruitt, who is spearheading a push to relax or undo Obama-era environmental rules, said in March he would no longer allow the agency to use studies with nonpublic scientific data to develop rules on public health and pollution. Scientists and environmentalists have argued that this would constrain key research because many public health and pollution studies rely on confidential medical information.

Pruitt had instructed staff to complete the guidelines by the end of February, according to the emails obtained by scientific advocacy group Union of Concerned Scientists and shared with Reuters. On Friday, the guidelines were submitted for review at the White House Office of Management and Budget.

In the emails, EPA officials discussed how new guidelines could complicate the way companies submit data. EPA relies on scientific research underpinned by sensitive medical and public health information or confidential industry data to craft rules to reduce chemical exposure and combat air and water pollution.

"This directive needs to be revised," Nancy Beck, head of EPA's chemicals office, wrote in a Jan. 31 email. "Without change it will jeopardize our entire pesticide registration/re-registration review process and likely all TSCA risk evaluations."

She was referring to the Toxic Substances Control Act (TSCA), which requires chemical companies to submit large volumes of data largely classified as confidential business information (CBI).

Making this data publicly available would be "incredibly burdensome" and impractical, Beck said.

In response, Richard Yamada, deputy assistant administrator in the EPA office of research, wrote that he "didn't know about the intricacies of CBI."

"We will need to thread this one real tight! Thanks Nancy!" he said.

Michael Halpern of the Union of Concerned Scientists said in an interview the emails show that EPA political staff concerns over protecting certain companies' trade secrets from public scrutiny are at odds with Pruitt's call for more transparency.

"They want special treatment for industry while showing no concerns for sensitive medical information or public health," he said.

EPA spokeswoman Liz Bowman said on Friday "any standards for protecting confidential business information would be the same for all stakeholders."

The emails show senior political EPA officials had been working with Republicans on the U.S. House of Representatives science committee since January on the new policy. It is likely to be based on similar legislation passed by the House three times that never got a Senate vote.